All inbound emails are stuck in exchange queue. Emails send to external domains are transporting without any issue.

Can you please tell me what exchange version are you using ? and What's the error message followed in the queue? Please try to improve the Diagnostic Logging on the MSExchangeTransport, then try to check the Event Log. PLs check the Event Viewer and see if there are errors related to same. Thanks

I am using exchange 2010, please find the error message when click on local queues. The remote pipeline has been stopped. It was running the command 'get-message -ResultSize '1000' - ReturnPageInfo $True -SortOrder '+FromAddress' -server 'myserver.mydomain.loc' -SearchForward $True - BookmarkObject $null .............

Did you try restart Transport service in Exchange and then test mail flow See if the below post helps you http://social.technet.microsoft.com/Forums/en-US/exchangesvrtransport/thread/51ca0cb0-579d-43fc-aff2-dc7c8341d34c